Hi James, I read your original question more carefully, and it looks like you want a separate followed by a join to have the same sub-object ordering as the original pre-separated object? Unfortunately I don't think there will be any reliable way to control that, the join process does not try to preserve ordering, it just combines faces into one brep and then goes through unjoined edges, comparing them to other unjoined edges, gluing them together if they are within tolerance. It's not surprising that some traces of the original order will remain but I don't think that it's going to be reliable.

One thing that might work for you though is to track things by setting object names on sub-objects. For example if you assign a unique object name to each edge of the original object, that name will come through the separate and rejoin process and so if the name was the index value in the original object you could recover the original index that way. I think that should work for both face and edge sub-objects.

- Michael